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- PDB-7sg1: XPA5 TCR in complex with HLA-DQ2-alpha1 -

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Basic information

Entry
Database: PDB / ID: 7sg1
TitleXPA5 TCR in complex with HLA-DQ2-alpha1
Components
  • (T-cell receptor, xpa5, ...) x 2
  • DQ2-glia-alpha1a peptide
  • HLA class II histocompatibility antigen, DQ alpha 1 chain
  • MHC class II HLA-DQ-beta-1
KeywordsIMMUNE SYSTEM / TCR-pMHC / Celiac disease
Function / homology
Function and homology information


MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane ...MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Co-inhibition by PD-1 / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / adaptive immune response / endosome membrane / immune response / Golgi membrane / lysosomal membrane / membrane / plasma membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class II HLA-DQ-beta-1 / HLA class II histocompatibility antigen, DQ alpha 1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsCiacchi, L. / Farenc, C. / Petersen, J. / Reid, H.H. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural basis of T cell receptor specificity and cross-reactivity of two HLA-DQ2.5-restricted gluten epitopes in celiac disease.
Authors: Ciacchi, L. / Farenc, C. / Dahal-Koirala, S. / Petersen, J. / Sollid, L.M. / Reid, H.H. / Rossjohn, J.
History
DepositionOct 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: MHC class II HLA-DQ-beta-1
F: HLA class II histocompatibility antigen, DQ alpha 1 chain
G: MHC class II HLA-DQ-beta-1
D: T-cell receptor, xpa5, alpha chain
E: T-cell receptor, xpa5, beta chain
C: DQ2-glia-alpha1a peptide
H: DQ2-glia-alpha1a peptide
I: T-cell receptor, xpa5, alpha chain
J: T-cell receptor, xpa5, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,95217
Polymers194,24310
Non-polymers7097
Water00
1
A: HLA class II histocompatibility antigen, DQ alpha 1 chain
B: MHC class II HLA-DQ-beta-1
D: T-cell receptor, xpa5, alpha chain
E: T-cell receptor, xpa5, beta chain
C: DQ2-glia-alpha1a peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4859
Polymers97,1215
Non-polymers3634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class II histocompatibility antigen, DQ alpha 1 chain
G: MHC class II HLA-DQ-beta-1
H: DQ2-glia-alpha1a peptide
I: T-cell receptor, xpa5, alpha chain
J: T-cell receptor, xpa5, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4678
Polymers97,1215
Non-polymers3453
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.602, 75.558, 216.804
Angle α, β, γ (deg.)90.000, 103.760, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain F and (resid 1 through 180 or resid 201 through 202))
12chain B
22chain G
13chain C
23chain H
14(chain E and (resid 2 through 192 or resid 199 through 256))
24chain J

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ILEILEPROPROchain AAA1 - 1803 - 182
211ILEILEPROPRO(chain F and (resid 1 through 180 or resid 201 through 202))FC1 - 1803 - 182
221NAGNAGEDOEDO(chain F and (resid 1 through 180 or resid 201 through 202))FN - O201 - 202
112SERSERTRPTRPchain BBB3 - 18813 - 198
212SERSERALAALAchain GGD3 - 19013 - 200
113GLNGLNSERSERchain CCG0 - 142 - 16
213GLNGLNSERSERchain HHH0 - 142 - 16
114ALAALAGLUGLU(chain E and (resid 2 through 192 or resid 199 through 256))EF2 - 19216 - 194
124SERSERALAALA(chain E and (resid 2 through 192 or resid 199 through 256))EF199 - 256201 - 258
214ALAALAALAALAchain JJJ2 - 25616 - 258

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules AFBG

#1: Protein HLA class II histocompatibility antigen, DQ alpha 1 chain / DC-1 alpha chain / DC-alpha / HLA-DCA / MHC class II DQA1


Mass: 20683.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01909
#2: Protein MHC class II HLA-DQ-beta-1


Mass: 23355.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O19712

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T-cell receptor, xpa5, ... , 2 types, 4 molecules DIEJ

#3: Protein T-cell receptor, xpa5, alpha chain


Mass: 22661.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#4: Protein T-cell receptor, xpa5, beta chain


Mass: 28747.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Protein/peptide / Sugars , 2 types, 4 molecules CH

#5: Protein/peptide DQ2-glia-alpha1a peptide


Mass: 1673.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper)
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 5 molecules

#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Mother liquor: 16-18% PEG3350, 0.12-0.14 M CaOAc, 0.1 M Tris/HCl at pH 8.0, Additives: 2 mM reduced and oxidised Glutathione

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 20, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→45.42 Å / Num. obs: 39655 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.976 / Net I/σ(I): 6
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3907 / CC1/2: 0.529 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MFG, 4OZI

6mfg

4ozi


Resolution: 3.1→45.42 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 1990 5.02 %
Rwork0.2165 37641 -
obs0.2187 39631 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.55 Å2 / Biso mean: 64.3531 Å2 / Biso min: 28.82 Å2
Refinement stepCycle: final / Resolution: 3.1→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12502 0 42 0 12544
Biso mean--81.48 --
Num. residues----1572
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1697X-RAY DIFFRACTION9.981TORSIONAL
12F1697X-RAY DIFFRACTION9.981TORSIONAL
21B1756X-RAY DIFFRACTION9.981TORSIONAL
22G1756X-RAY DIFFRACTION9.981TORSIONAL
31C138X-RAY DIFFRACTION9.981TORSIONAL
32H138X-RAY DIFFRACTION9.981TORSIONAL
41E2126X-RAY DIFFRACTION9.981TORSIONAL
42J2126X-RAY DIFFRACTION9.981TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.1-3.180.35871410.310426702811
3.18-3.260.31431380.290726892827
3.26-3.360.29661450.257626062751
3.36-3.470.35811390.26126922831
3.47-3.590.33931480.258626872835
3.59-3.740.29571440.248926842828
3.74-3.910.31111410.243626602801
3.91-4.110.27521390.214826702809
4.11-4.370.23531480.189526912839
4.37-4.710.17381380.161926702808
4.71-5.180.18941390.162126982837
5.18-5.930.22321450.187726962841
5.93-7.460.2291450.225127332878
7.46-45.420.25621400.209327952935
Refinement TLS params.Method: refined / Origin x: -37.2491 Å / Origin y: 29.8617 Å / Origin z: 53.2821 Å
111213212223313233
T0.4518 Å2-0.0694 Å20.0657 Å2-0.4328 Å20.0446 Å2--0.3642 Å2
L1.1416 °20.1016 °20.8831 °2-0.2653 °20.101 °2--0.7562 °2
S0.0096 Å °-0.3513 Å °-0.0489 Å °0.1253 Å °-0.025 Å °-0.0265 Å °-0.0666 Å °-0.2738 Å °-0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 180
2X-RAY DIFFRACTION1allA201 - 202
3X-RAY DIFFRACTION1allB3 - 188
4X-RAY DIFFRACTION1allF0 - 180
5X-RAY DIFFRACTION1allF201 - 301
6X-RAY DIFFRACTION1allG3 - 190
7X-RAY DIFFRACTION1allD2 - 218
8X-RAY DIFFRACTION1allE2 - 257
9X-RAY DIFFRACTION1allC0 - 14
10X-RAY DIFFRACTION1allH0 - 14
11X-RAY DIFFRACTION1allI4 - 194
12X-RAY DIFFRACTION1allJ2 - 256
13X-RAY DIFFRACTION1allK1 - 2

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